Positive selection of an MHC class-I restricted TCR in the absence of classical MHC class I molecules

The H-2Ld alloreactive 2C T cell receptor (TCR) is commonly considered as being positively selected on the H-2Kb molecule. Surprisingly, 2C TCR+ CD8+ single-positive T cells emerge in massive numbers in fetal thymic organ culture originating from 2C transgenic, H-2KbDb−/− (2C+KbDb−/−) but not in fetal thymic organ culture from β2-microglobulin−/− 2C transgenic animals. Mature CD8+ T cells are observed in newborn but not in adult 2C+KbDb−/− mice. These CD8+ T cells express the α4β7 integrin, which allows them to populate the intestine, a pattern of migration visualized by intrathymic injection of FITC and subsequent accrual of FITC-labeled lymphocytes in the gut. We conclude that the 2C TCR is reactive not only with H-2Ld and H-2Kb, but also with nonclassical MHC class I products to enable positive selection of 2C+ T cells in the fetal and newborn thymus and to support their maintenance in the intestine.

Short-Lived and Phosphorylated Proteins Contribute to Carrier-Mediated Efflux, but Not to Influx, of Auxin in Suspension-Cultured Tobacco Cells1

Auxin is transported across the plasma membrane of plant cells by diffusion and by two carriers operating in opposite directions, the influx and efflux carriers. Both carriers most likely play an important role in controlling auxin concentration and distribution in plants but little is known regarding their regulation. We describe the influence of modifications of the transmembrane pH gradient and the effect of agents interfering with protein synthesis, protein traffic, and protein phosphorylation on the activity of the auxin carriers in suspension-cultured tobacco (Nicotiana tabacum L.) cells. Carrier-mediated influx and efflux were monitored independently by measuring the accumulation of [14C]2,4-dichlorophenoxyacetic acid and [3H]naphthylacetic acid, respectively. The activity of the influx carrier decreased on increasing external pH and on decreasing internal pH, whereas that of the efflux carrier was only impaired on internal acidification. The efflux carrier activity was inhibited by cycloheximide, brefeldin A, and the protein kinase inhibitors staurosporine and K252a, as shown by the increased capability of treated cells to accumulate [3H]naphthylacetic acid. Kinetics and reversibility of the effect of brefeldin A were consistent with one or several components of the efflux system being turned over at the plasma membrane with a half-time of less than 10 min. Inhibition of efflux by protein kinase inhibitors suggested that protein phosphorylation was essential to sustain the activity of the efflux carrier. On the contrary, the pharmacological agents used in this study failed to inhibit [14C]2,4-dichlorophenoxyacetic acid accumulation, suggesting that rapidly turned-over proteins or proteins activated by phosphorylation are not essential to carrier-mediated auxin influx. Our data support the idea that the efflux carrier in plants constitutes a complex system regulated at multiple levels, in marked contrast with the influx carrier. Physiological implications of the kinetic features of this regulation are discussed.

Pleadings of mercy for the animal world, and all other defenseless creatures /

Photocopy.

Ras plasma membrane signalling platforms

The plasma membrane is a complex, dynamic structure that provides platforms for the assembly of many signal transduction pathways. These platforms have the capacity to impose an additional level of regulation on cell signalling networks. In this review, we will consider specifically how Ras proteins interact with the plasma membrane. The focus will be on recent studies that provide novel spatial and dynamic insights into the micro-environments that different Ras proteins utilize for signal transduction. We will correlate these recent studies suggesting Ras proteins might operate within a heterogeneous plasma membrane with earlier biochemical work on Ras signal transduction.

Intracellular protein determination using droplet-based immunoassays

This paper describes the implementation of a sensitive, on-chip immunoassay for the analysis of intracellular proteins, developed using microdroplet technology. The system offers a number of analytical functionalities, enabling the lysis of low cell numbers, as well as protein detection and quantification, integrated within a single process flow. Cells were introduced into the device in suspension and were electrically lysed in situ. The cell lysate was subsequently encapsulated together with antibody-functionalized beads into stable, water-in-oil droplets, which were stored on-chip. The binding of intracellular proteins to the beads was monitored fluorescently. By analyzing many individual droplets and quantifying the data obtained against standard additions, we measured the level of two intracellular proteins, namely, HRas-mCitrine, expressed within HEK-293 cells, and actin-EGFP, expressed within MCF-7 cells. We determined the concentrations of these proteins over 5 orders of magnitude, from ~50 pM to 1 µM. The results from this semiautomated method were compared to those for determinations made using Western blots, and were found not only to be faster, but required a smaller number of cells. © 2011 American Chemical Society.

Nuclear magnetic resonance spectroscopy and ultrasound

The work described in this thesis is directed to the examination of the hypothesis that ultrasound may be used to perturb molecular motion in the liquid phase. These changes can then be detected by nuclear magnetic resonance (NMR) in spin-lattice and spin-spin relaxation times. The objective being to develop a method capable of reducing the pulsed NMR acquisition times of slowly relaxing nuclei. The thesis describes the theoretical principles underlying both NMR spectroscopy and ultrasonics with particular attention being paid to factors that impinge on testing the above hypothesis. Apparatus has been constructed to enable ultrasound at frequencies between 1 and 10 mega-hertz with a variable power up to 100W/cm-2 to be introduced in the NMR sample. A broadband high frequency generator is used to drive PZT piezo-electric transducer via various transducer to liquid coupling arrangements. A commercial instrument of 20 kilo-hertz has also been employed to test the above hypothesis and also to demonstrate the usefulness of ultrasound in sonochemistry. The latter objective being, detection of radical formation in monomer and polymer ultrasonic degradation. The principle features of the results obtained are: Ultrasonic perturbation of T1 is far smaller for pure liquids than is for mixtures. The effects appear to be greater on protons (1H) than on carbon-13 nuclei (13C) relaxation times. The observed effect of ultrasonics is not due to temperature changes in the sample. As the power applied to the transducer is progressively increased T1 decreases to a minimum and then increases. The T1's of the same nuclei in different functional groups are influenced to different extents by ultrasound. Studies of the 14N resonances from an equimolar mixture of N, N-dimethylformamide and deuterated chloroform with ultrasonic frequencies at 1.115, 6, 6.42 and 10 MHz show that as the frequency is increased the NMR signal to noise ratio decreases to zero at the Larmor frequency of 6.42 MHz and then again rises. This reveals the surprising indication that an effect corresponding to nuclear acoustic saturation in the liquid may be observable. Ultrasonic irradiation of acidified ammonium chloride solution at and around 6.42 MHz appears to cause distinctive changes in the proton-nitrogen J coupling resonance at 89.56 MHz. Ultrasonic irradiation of N, N-dimethylacetamide at 2 KHz using the lowest stable power revealed the onset of coalescence in the proton spectrum. The corresponding effect achieved by direct heating required a temperature rise of approximately 30oC. The effects of low frequency (20 KHz) on relaxation times appear to be nil. Detection of radical formation proved difficult but is still regarded as the principle route for monomer and polymer degradation. The initial hypothesis is considered proven with the results showing significant changes in the mega-hertz region and none at 20 KHz.

Prodrugs of antiviral phosphonates

Phosphonoformate and phosphonoacetate are effective antiviral agents, however they are charged at physiological pH and as such penetration into cells and diffusion across the blood-brain bamer is limited. In an attempt to increase the lipophilicity and improve the transport properties of these molecules, prodrugs were synthesised and their stabilities and reconversion to the parent compound subsequently investigated by the techniques of 31P nuclear magnetic resonance spectroscopy and high performance liquid Chromatography. A series of 4-substituted dibenzyl (methoxycarbonyl)phosphonates were prepared and found to be hydrolytically unstable giving predominantly the diesters, benzyl (methoxycarbonyl)phosphonates. This instability arose from the electron-withdrawing effect of the carbonyl group promoting nucleophilic attack at phosphorus. It was possible to influence the mechanism and, to some extent, the rate of hydrolysis of the phosphonoformate triesters to the diesters by varying the electronic nature of the substituent in the 4-position of the aromatic ring. Strongly electron-withdrawing groups increased the sensitivity of phosphorus to nucleophilic attack, thus promoting P-O .bond cleavage and rapid hydrolysis. Conversely, weakly electron-withdrawing substituents encouraged C-O bond fission, presumably through resonance stabilisation of the benzyl carbonium ion. The loss of the protecting group on phosphorus was in competition with nucleophilic attack at the carbonyl group, resulting in P-C bond cleavage with dibenzyl phosphite formation. The high instability and P-C bond fission make triesters unsuitable prodrug forms of phosphonoformate. A range of chemically stable triesters of phosphonoacetate were synthesised and their bioactivation investigated. Di(benzoyloxymethyl) (methoxycarbonylmethyl)phosphonates degraded to the relevant benzoyloxymethyl (methoxycarbonylmethyl)phosphonate in the presence of esterase. The enzymatic activation was restricted to the removal of only one protecting group from phosphorus, most likely due to the close proximity of the benzoyloxy ester function to the anionic charge on the diester. However, in similar systems di(4-alkanoyloxybenzyl) (methoxycarbonylmethyl)phosphonates degraded in the presence of esterase with the loss of both protecting groups on phosphorus to give the monoester, (methoxycarbonylmethyl)phosphonate, via the intermediary of the unstable 4-hydroxy benzyl esters. The methoxycarbonyl function remained intact. The rate of enzymatic hydrolysis and subsequent removal of the protecting groups on phosphorus was dependent on the nature of the alkanoyl group and was most rapid for the 4-nbutanoyloxybenzyl and 4-iso-butanoyloxybenzyl esters of phosphonoacetate. This provides a strategy for the design of a prodrug with sufficient stability in plasma to reach the central nervous system in high concentration, wherein rapid metabolism to the active drug by brain-associated enzymes occurs.

Abaxial Anthocyanin Layer in Leaves of Tropical Rain Forest Plants: Enhancer of Light Capture in Deep Shade

The permanent pigmentation of the leaves of tropical rain forest herbs with anthocyanin has traditionally been viewed as a mechanism for enhancing transpiration by increased heat absorption. We report measurements to ?+0.1?0C on four Indo-mal- esian forest species polymorphic with respect to color. There were no detectable differences in temperature between cyanic and green leaves. In deeply shaded habitats, any temperature difference would arise from black-body infrared radiation which all leaves absorb and to which anthocyanins are transparent. Reflectance spectra of the lower leaf surfaces of these species re- vealed increased reflectance around 650-750 nm for cyanic leaves compared with green leaves of the same species. In all spe- cies anthocyanin was located in a single layer of cells immediately below the photosynthetic tissue. These observations provide empirical evidence that the cyanic layer can improve photosynthetic energy capture by back-scattering additional light through the photosynthetic tissue.

A Binaural Cochlear Implant Sound Coding Strategy Inspired by the Contralateral Medial Olivocochlear Reflex.

OBJECTIVES: In natural hearing, cochlear mechanical compression is dynamically adjusted via the efferent medial olivocochlear reflex (MOCR). These adjustments probably help understanding speech in noisy environments and are not available to the users of current cochlear implants (CIs). The aims of the present study are to: (1) present a binaural CI sound processing strategy inspired by the control of cochlear compression provided by the contralateral MOCR in natural hearing; and (2) assess the benefits of the new strategy for understanding speech presented in competition with steady noise with a speech-like spectrum in various spatial configurations of the speech and noise sources. DESIGN: Pairs of CI sound processors (one per ear) were constructed to mimic or not mimic the effects of the contralateral MOCR on compression. For the nonmimicking condition (standard strategy or STD), the two processors in a pair functioned similarly to standard clinical processors (i.e., with fixed back-end compression and independently of each other). When configured to mimic the effects of the MOCR (MOC strategy), the two processors communicated with each other and the amount of back-end compression in a given frequency channel of each processor in the pair decreased/increased dynamically (so that output levels dropped/increased) with increases/decreases in the output energy from the corresponding frequency channel in the contralateral processor. Speech reception thresholds in speech-shaped noise were measured for 3 bilateral CI users and 2 single-sided deaf unilateral CI users. Thresholds were compared for the STD and MOC strategies in unilateral and bilateral listening conditions and for three spatial configurations of the speech and noise sources in simulated free-field conditions: speech and noise sources colocated in front of the listener, speech on the left ear with noise in front of the listener, and speech on the left ear with noise on the right ear. In both bilateral and unilateral listening, the electrical stimulus delivered to the test ear(s) was always calculated as if the listeners were wearing bilateral processors. RESULTS: In both unilateral and bilateral listening conditions, mean speech reception thresholds were comparable with the two strategies for colocated speech and noise sources, but were at least 2 dB lower (better) with the MOC than with the STD strategy for spatially separated speech and noise sources. In unilateral listening conditions, mean thresholds improved with increasing the spatial separation between the speech and noise sources regardless of the strategy but the improvement was significantly greater with the MOC strategy. In bilateral listening conditions, thresholds improved significantly with increasing the speech-noise spatial separation only with the MOC strategy. CONCLUSIONS: The MOC strategy (1) significantly improved the intelligibility of speech presented in competition with a spatially separated noise source, both in unilateral and bilateral listening conditions; (2) produced significant spatial release from masking in bilateral listening conditions, something that did not occur with fixed compression; and (3) enhanced spatial release from masking in unilateral listening conditions. The MOC strategy as implemented here, or a modified version of it, may be usefully applied in CIs and in hearing aids.

Tools For Spatiotemporally Specific Proteomic Analysis In Multicellular Organisms

The emergence of mass spectrometry-based proteomics has revolutionized the study of proteins and their abundances, functions, interactions, and modifications. However, in a multicellular organism, it is difficult to monitor dynamic changes in protein synthesis in a specific cell type within its native environment. In this thesis, we describe methods that enable the metabolic labeling, purification, and analysis of proteins in specific cell types and during defined periods in live animals. We first engineered a eukaryotic phenylalanyl-tRNA synthetase (PheRS) to selectively recognize the unnatural L-phenylalanine analog p-azido-L-phenylalanine (Azf). Using Caenorhabditis elegans, we expressed the engineered PheRS in a cell type of choice (i.e. body wall muscles, intestinal epithelial cells, neurons, pharyngeal muscles), permitting proteins in those cells -- and only those cells -- to be labeled with azides. Labeled proteins are therefore subject to "click" conjugation to cyclooctyne-functionalized affnity probes, separation from the rest of the protein pool and identification by mass spectrometry. By coupling our methodology with heavy isotopic labeling, we successfully identified proteins -- including proteins with previously unknown expression patterns -- expressed in targeted subsets of cells. While cell types like body wall or pharyngeal muscles can be targeted with a single promoter, many cells cannot; spatiotemporal selectivity typically results from the combinatorial action of multiple regulators. To enhance spatiotemporal selectivity, we next developed a two-component system to drive overlapping -- but not identical -- patterns of expression of engineered PheRS, restricting labeling to cells that express both elements. Specifically, we developed a split-intein-based split-PheRS system for highly efficient PheRS-reconstitution through protein splicing. Together, these tools represent a powerful approach for unbiased discovery of proteins uniquely expressed in a subset of cells at specific developmental stages.

Hall Effect and transient surface photovoltage (SPV) study of Cu3BiS3 thin films

Se presentan las propiedades eléctricas del compuesto Cu3BiS3 depositado por co-evaporación. Este es un nuevo compuesto que puede tener propiedades adecuadas para ser utilizado como capa absorbente en celdas solares. Las muestras fueron caracterizadas a través de medidas de efecto Hall y fotovoltaje superficial transiente (SPV). A través de medidas de efecto Hall se encontró que la concentración de portadores de carga n es del orden de 1016 cm-3 independiente de la relación de masas de Cu/Bi. También se encontró que la movilidad de este compuesto (μ del orden de 4 cm2V -1s-1) varía de acuerdo con los mecanismos de transporte que la gobiernan en dependencia con la temperatura. A partir de las medidas de SPV se encontró alta densidad de defectos superficiales, defectos que son pasivados al superponer una capa buffer sobre el compuesto Cu3BiS3.

Measuring macromolecular diffusion using heteronuclear multiple-quantum pulsed-field-gradient NMR

We have previously shown that H-1 pulsed-field-gradient (PFG) NMR spectroscopy provides a facile method for monitoring protein self-association and can be used, albeit with some caveats, to measure the apparent molecular mass of the diffusant [Dingley et al. (1995) J. Biomol. NMR, 6, 321-328]. In this paper we show that, for N-15-labelled proteins, selection of H-1-N-15 multiple-quantum (MQ) coherences in PFG diffusion experiments provides several advantages over monitoring H-1 single-quantum (SQ) magnetization. First, the use of a gradient-selected MQ filter provides a convenient means of suppressing resonances from both the solvent and unlabelled solutes. Second, H-1-N-15 zero-quantum coherence dephases more rapidly than H-1 SQ coherence under the influence of a PFG. This allows the diffusion coefficients of larger proteins to be measured more readily. Alternatively, the gradient length and/or the diffusion delay may be decreased, thereby reducing signal losses from relaxation. In order to extend the size of macromolecules to which these experiments can be applied, we have developed a new MQ PFG diffusion experiment in which the magnetization is stored as longitudinal two-spin order for most of the diffusion period, thus minimizing sensitivity losses due to transverse relaxation and J-coupling evolution.

Application of NMR RDC’s, relaxation and self-diffusion for the study of dynamic processes of small molecules in solution

Spin-lattice Relaxation, self-Diffusion coefficients and Residual Dipolar Couplings (RDC’s) are the basis of well established Nuclear Magnetic Resonance techniques for the physicochemical study of small molecules (typically organic compounds and natural products with MW < 1000 Da), as they proved to be a powerful and complementary source of information about structural dynamic processes in solution. The work developed in this thesis consists in the application of the earlier-mentioned NMR techniques to explore, analyze and systematize patterns of the molecular dynamic behavior of selected small molecules in particular experimental conditions. Two systems were chosen to investigate molecular dynamic behavior by these techniques: the dynamics of ion-pair formation and ion interaction in ionic liquids (IL) and the dynamics of molecular reorientation when molecules are placed in oriented phases (alignment media). The application of NMR spin-lattice relaxation and self-diffusion measurements was applied to study the rotational and translational molecular dynamics of the IL: 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4]. The study of the cation-anion dynamics in neat and IL-water mixtures was systematically investigated by a combination of multinuclear NMR relaxation techniques with diffusion data (using by H1, C13 and F19 NMR spectroscopy). Spin-lattice relaxation time (T1), self-diffusion coefficients and nuclear Overhauser effect experiments were combined to determine the conditions that favor the formation of long lived [BMIM][BF4] ion-pairs in water. For this purpose and using the self-diffusion coefficients of cation and anion as a probe, different IL-water compositions were screened (from neat IL to infinite dilution) to find the conditions where both cation and anion present equal diffusion coefficients (8% water fraction at 25 ºC). This condition as well as the neat IL and the infinite dilution were then further studied by 13C NMR relaxation in order to determine correlation times (c) for the molecular reorientational motion using a mathematical iterative procedure and experimental data obtained in a temperature range between 273 and 353 K. The behavior of self-diffusion and relaxation data obtained in our experiments point at the combining parameters of molar fraction 8 % and temperature 298 K as the most favorable condition for the formation of long lived ion-pairs. When molecules are subjected to soft anisotropic motion by being placed in some special media, Residual Dipolar Couplings (RDCs), can be measured, because of the partial alignment induced by this media. RDCs are emerging as a powerful routine tool employed in conformational analysis, as it complements and even outperforms the approaches based on the classical NMR NOE or J3 couplings. In this work, three different alignment media have been characterized and evaluated in terms of integrity using 2H and 1H 1D-NMR spectroscopy, namely the stretched and compressed gel PMMA, and the lyotropic liquid crystals CpCl/n-hexanol/brine and cromolyn/water. The influence that different media and degrees of alignment have on the dynamic properties of several molecules was explored. Different sized sugars were used and their self-diffusion was determined as well as conformation features using RDCs. The results obtained indicate that no influence is felt by the small molecules diffusion and conformational features studied within the alignment degree range studied, which was the 3, 5 and 6 % CpCl/n-hexanol/brine for diffusion, and 5 and 7.5 % CpCl/n-hexanol/brine for conformation. It was also possible to determine that the small molecules diffusion verified in the alignment media presented close values to the ones observed in water, reinforcing the idea of no conditioning of molecular properties in such media.

Radial and longitudinal diffusion of myoglobin in single living heart and skeletal muscle cells

We have used a fluorescence recovery after photobleaching (FRAP) technique to measure radial diffusion of myoglobin and other proteins in single skeletal and cardiac muscle cells. We compare the radial diffusivities, Dr (i.e., diffusion perpendicular to the long fiber axis), with longitudinal ones, Dl (i.e., parallel to the long fiber axis), both measured by the same technique, for myoglobin (17 kDa), lactalbumin (14 kDa), and ovalbumin (45 kDa). At 22°C, Dl for myoglobin is 1.2 × 10−7 cm2/s in soleus fibers and 1.1 × 10−7 cm2/s in cardiomyocytes. Dl for lactalbumin is similar in both cell types. Dr for myoglobin is 1.2 × 10−7 cm2/s in soleus fibers and 1.1 × 10−7 cm2/s in cardiomyocytes and, again, similar for lactalbumin. Dl and Dr for ovalbumin are 0.5 × 10−7 cm2/s. In the case of myoglobin, both Dl and Dr at 37°C are about 80% higher than at 22°C. We conclude that intracellular diffusivity of myoglobin and other proteins (i) is very low in striated muscle cells, ≈1/10 of the value in dilute protein solution, (ii) is not markedly different in longitudinal and radial direction, and (iii) is identical in heart and skeletal muscle. A Krogh cylinder model calculation holding for steady-state tissue oxygenation predicts that, based on these myoglobin diffusivities, myoglobin-facilitated oxygen diffusion contributes 4% to the overall intracellular oxygen transport of maximally exercising skeletal muscle and less than 2% to that of heart under conditions of high work load.

Nmr imaging of the diffusion of water into poly(tetrahydrofurfuryl methacrylate-co-hydroxyethyl methacrylate)

0Nuclear magnetic resonance (n.m.r.) imaging was used to study the ingress of water into poly(tetrahydrofurfuryl methacrylate-co-hydroxyethyl methacrylate). The study offers strong evidence that the diffusion is Fickian in nature. The diffusion coefficient, D, obtained by fitting the underlying diffusion profile, attainable from the images, according to the equation for Fickian diffusion, is 1.5 x 10(-11) m(2) s(-1), which is in good correlation with the value of 2.1 x 10(-11) m(2) s(-1), obtained from mass uptake measurements. Additionally, from the T-2-weighted images, Superimposed features observed in addition to the underlying Fickian diffusion profiles were shown to have a longer spin-spin relaxation time, T-2. This Suggests the presence of two types of water within the polymer matrix; a less mobile phase of absorbed water that is interacting strongly with the polymer matrix and a more mobile phase of absorbed water residing within the cracks observed in the environmental scanning electron micrograph. (C) 1997 Elsevier Science Ltd.